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Made mdrun -pforce terminate with non-finite forces
2016-12-08
Be
r
k H
e
ss
Made mdrun -pforce
t
e
rminate w
i
th n
o
n-finite fo
r
ces
commit
|
commitdiff
|
tree
2016-11-24
Be
r
k Hess
Change spline moduli calcul
a
tion to double
commit
|
commitdiff
|
tree
2016-11-23
Berk Hes
s
Co
n
vert ener
g
yhistory_t to use
s
t
d::
v
e
c
t
or
commit
|
commitdiff
|
tree
2016-11-23
Berk
H
ess
U
s
e templating in c
h
eckpoint
.
cpp
commit
|
commitdiff
|
tree
2016-11-01
Berk
H
ess
Fix time
l
a
b
el print
in gmx van
h
ove
commit
|
commitdiff
|
tree
2016-10-29
Berk Hess
Ad
d
gmx du
m
p
option for
p
rinting
parameters
commit
|
commitdiff
|
tree
2016-10-28
Berk Hess
DLB can now
t
u
rn off, when
slower
commit
|
commitdiff
|
tree
2016-10-28
Berk Hess
Fix DLB timing
w
ith CUDA
and Ope
n
CL
commit
|
commitdiff
|
tree
2016-10-15
B
erk Hess
M
o
ve e
n
e
rgyhis
t
or
y
_t
o
ut of t_state
commit
|
commitdiff
|
tree
2016-10-14
B
e
r
k Hess
A
p
ply Ber
e
n
d
s
e
n P-
c
ouple at nst
p
couple steps
commit
|
commitdiff
|
tree
2016-10-13
Berk H
e
ss
Exte
n
d mtop_loo
k
up
.
h
commit
|
commitdiff
|
tree
2016-10-12
B
e
rk Hess
Fixed exception in
u
sused result
commit
|
commitdiff
|
tree
2016-10-12
Berk Hess
Fixed print bug in g
m
x wham
commit
|
commitdiff
|
tree
2016-10-12
Berk Hess
R
e
f
actor NPT
e
ne
r
g
y calc
u
lation
commit
|
commitdiff
|
tree
2016-10-12
Berk Hess
Re
s
tructure leap-frog integ
r
a
t
ors
commit
|
commitdiff
|
tree
2016-10-11
Berk Hess
Speed up mtop_util atom look
u
p
commit
|
commitdiff
|
tree
2016-10-08
Berk Hess
Add readC
o
n
f
AndTopology
commit
|
commitdiff
|
tree
2016-10-07
Berk Hess
Cha
n
ged fr
-
>f_novi
r
sum to Pad
d
edRVecVector
commit
|
commitdiff
|
tree
2016-10-01
Berk H
e
ss
Fix
i
nputr
e
c initialization in 4 tools
commit
|
commitdiff
|
tree
2016-09-29
Berk Hess
Use std:
:
vector i
n
t
_
state
commit
|
commitdiff
|
tree
2016-09-29
Berk Hess
Add
f
lags for o
p
tio
n
a
l
t_atoms entries
commit
|
commitdiff
|
tree
2016-09-22
B
erk Hess
Fix gcc warning
i
n
A
lig
n
ed
A
llocator
commit
|
commitdiff
|
tree
2016-09-20
Berk Hess
Remove state duplication in serial run
s
commit
|
commitdiff
|
tree
2016-09-16
Berk Hess
Fixed unused variables in domdec
.
cpp
commit
|
commitdiff
|
tree
2016-09-16
Berk Hess
Mer
g
e b
r
anch rele
a
se-2
0
1
6
commit
|
commitdiff
|
tree
2016-09-16
Berk
He
s
s
Made dista
n
c
e restraints work
with
t
hreads and DD
commit
|
commitdiff
|
tree
2016-09-13
Berk Hess
Moved expanded ensemble history to pointer
in t_
s
tate
commit
|
commitdiff
|
tree
2016-09-13
B
erk Hess
Chan
g
e
E
D an
d
swapstate to pointers in t_s
t
ate
commit
|
commitdiff
|
tree
2016-09-12
Berk
Hess
A
d
d const to th
r
ead
-
MPI functions
commit
|
commitdiff
|
tree
2016-09-10
Berk H
e
ss
Remo
v
e
c
on
t
inuati
o
n
from c
o
nvert_tpr
commit
|
commitdiff
|
tree
2016-09-06
Berk
Hess
Fi
x
bug
with conjug
a
t
e
-gradient and OpenM
P
commit
|
commitdiff
|
tree
2016-09-06
Be
r
k Hess
Cons
o
lidate MD algori
t
hm
a
tom se
t
up
commit
|
commitdiff
|
tree
2016-09-05
Berk Hess
Re-enabl
e
flexibl
e
constraint
s
with DD
commit
|
commitdiff
|
tree
2016-09-04
Berk Hess
Merge branch release-2
0
16
commit
|
commitdiff
|
tree
2016-09-03
B
e
rk Hess
Clea
n
up
PME fl
a
gs
v
ariable
u
se
commit
|
commitdiff
|
tree
2016-09-02
Berk He
s
s
Merge b
r
anch
rel
e
ase-5-1 into release-20
1
6
commit
|
commitdiff
|
tree
2016-09-02
B
erk Hess
Fix Pa
r
rinel
l
o-
R
ahman wi
t
h nstpcouple>
1
commit
|
commitdiff
|
tree
2016-08-30
Ber
k
H
ess
Make virial reproduci
b
le
commit
|
commitdiff
|
tree
2016-08-27
Berk Hes
s
Reduce roun
d
ing errors
in SETTLE
commit
|
commitdiff
|
tree
2016-08-24
Berk
H
ess
F
ix Ewald su
r
fac
e
+3DC
c
orrections
commit
|
commitdiff
|
tree
2016-08-24
Berk Hess
Merge bran
c
h release-
5
-1 into release-2
0
16
commit
|
commitdiff
|
tree
2016-08-23
Be
r
k
H
ess
Remove vari
a
ble p
r
ecision gro writing
commit
|
commitdiff
|
tree
2016-08-17
B
e
rk Hess
Fix
e
d openin
g
of wall table files
commit
|
commitdiff
|
tree
2016-08-15
Berk Hess
Reduce FE pair-l
i
st
m
emory us
a
ge
commit
|
commitdiff
|
tree
2016-08-10
Berk
Hes
s
Fix de
a
dlock with
t
hread-MPI
commit
|
commitdiff
|
tree
2016-08-09
Berk Hess
F
ix twin-cutoff for GPU L
J
pot-switch
commit
|
commitdiff
|
tree
2016-07-07
Berk Hess
Rel
a
x pu
l
l PB
C
check
commit
|
commitdiff
|
tree
2016-07-05
B
erk Hess
Add checks for
too much memo
r
y
in
g_nmeig
commit
|
commitdiff
|
tree
2016-07-03
B
e
rk Hess
Add grom
p
p check
for pull group
commit
|
commitdiff
|
tree
2016-06-28
Be
r
k
H
ess
Properly reset
C
U
D
A app
l
ication clock
s
commit
|
commitdiff
|
tree
2016-06-27
Berk Hess
Us
e
s
y
sconf
(
_SC_NPROCESSORS_ONLN)
commit
|
commitdiff
|
tree
2016-06-26
Berk Hess
Fix
v
site bug wit
h
MPI+OpenMP
commit
|
commitdiff
|
tree
2016-06-24
B
erk He
s
s
Fix Verl
e
t bu
f
fer c
a
lculation w
i
th nstlist=1
commit
|
commitdiff
|
tree
2016-06-23
Berk Hess
More accur
a
te GPU list spl
i
tting
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
U
pda
t
ed Open
C
L
TODOList
.
txt
commit
|
commitdiff
|
tree
2016-06-22
B
e
rk He
s
s
Add nbnx
n
pai
r
-list
rebalancin
g
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Remove Ope
n
MP overhead at high
paralleliza
t
ion
commit
|
commitdiff
|
tree
2016-06-22
Berk
H
ess
Correct GPU pa
i
r
es
t
im
a
te f
o
r
list spl
i
tting
commit
|
commitdiff
|
tree
2016-06-21
Berk Hess
Fix bug w
i
th fbpo
s
res
+
MPI+Op
e
nMP
commit
|
commitdiff
|
tree
2016-06-20
B
e
rk
H
e
s
s
I
ncreased tpx_inco
m
p
a
t
ible_v
e
rsion to 30
commit
|
commitdiff
|
tree
2016-06-19
Be
r
k
H
ess
Remove wa
r
n
ings on c
h
eckpoint mis
m
atch
commit
|
commitdiff
|
tree
2016-06-17
Berk
Hess
Rem
o
ve
st
d
::thread::hardware_concurrenc
y
()
commit
|
commitdiff
|
tree
2016-06-14
Berk Hes
s
Fix OpenCL error
w
ith
e
mp
t
y domains
commit
|
commitdiff
|
tree
2016-06-13
Berk Hess
Handle c
o
nst
r
ain
t
errors w
i
th EM
commit
|
commitdiff
|
tree
2016-06-07
Berk Hess
Fix data race in h
w
info
with thread-M
P
I
commit
|
commitdiff
|
tree
2016-06-03
Berk Hess
Handle pa
r
tially frozen and con
s
t
ra
i
ned atoms
commit
|
commitdiff
|
tree
2016-05-31
Be
r
k
H
e
ss
R
eposi
t
io
n
nbnxn fille
r
particles
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
A
v
oid num
e
rical overflow with o
v
erlapping atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk
H
e
ss
Ad
d
check f
o
r finite e
n
ergies
commit
|
commitdiff
|
tree
2016-05-30
Berk H
e
s
s
A
d
d gro
m
pp check for unboun
d
a
t
oms
commit
|
commitdiff
|
tree
2016-05-23
Berk Hess
Fix bug in v
-
rescale
thermostat &
r
eplica e
x
change
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
Optimized the vsite thre
a
di
n
g
commit
|
commitdiff
|
tree
2016-05-10
Berk
Hess
Fix CUDA shmem bug
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
S
upport cmap
w
ith QMMM
commit
|
commitdiff
|
tree
2016-05-08
B
e
r
k
Hess
Upda
t
e mdrun termina
t
ion
i
nfo
commit
|
commitdiff
|
tree
2016-05-06
Berk H
e
ss
O
penMP p
a
rallel
i
zation for pull
commit
|
commitdiff
|
tree
2016-04-20
Berk
H
e
ss
Fix pull leg
e
nd with extern
a
l potentia
l
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Al
l
ow
rcoulomb>rvdw with
P
ME
commit
|
commitdiff
|
tree
2016-04-19
B
e
rk Hess
Broadc
a
s
t
p
u
ll
external
potential pr
o
vid
e
r strin
g
commit
|
commitdiff
|
tree
2016-04-19
Berk Hes
s
Fix gmx hbond gr
o
up
o
v
erlap check
commit
|
commitdiff
|
tree
2016-04-14
Berk Hess
Add QMMM
checks
commit
|
commitdiff
|
tree
2016-04-03
B
erk Hess
Correct
n
rd
f
for 1
D
/
2
D
systems
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Fix incl
u
des in rea
d
p
u
l
l
.
cpp
commit
|
commitdiff
|
tree
2016-03-31
Berk He
s
s
Add
o
ption for external pull p
o
t
ential
commit
|
commitdiff
|
tree
2016-03-30
Berk Hes
s
Co
r
rect mdrun tMPI (non-)parallel error
message
commit
|
commitdiff
|
tree
2016-03-26
Berk He
s
s
Ad
d
real/S
I
MD template for LJ-14
p
airs
commit
|
commitdiff
|
tree
2016-03-22
B
erk He
s
s
A
voi
d
a
s
ser
t
io
n
failure in pme
_
loadbal
_
do
commit
|
commitdiff
|
tree
2016-03-22
B
er
k
Hess
Mak
e
gmx v
a
nhove work without PBC
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
LJ c
o
m
b
inati
o
n
r
ule k
e
rnels for CUDA
commit
|
commitdiff
|
tree
2016-03-21
Be
r
k Hess
Moved pull
initialization back to mdru
n
ner
commit
|
commitdiff
|
tree
2016-03-18
Berk Hess
F
i
x no
n
-norma
l
ization of FFT autocorr
commit
|
commitdiff
|
tree
2016-03-14
Berk Hess
Remove restriction on dihdraltype
s
o
rder
commit
|
commitdiff
|
tree
2016-03-12
B
erk He
s
s
Split off Fermi
kernel from CUDA
ker
n
el
commit
|
commitdiff
|
tree
2016-03-09
Berk Hess
Fix Ewald 3D
C
dipole
w
ith Verlet
scheme
commit
|
commitdiff
|
tree
2016-03-04
Berk
H
ess
Converte
d
csettle() to use real/SimdReal template
commit
|
commitdiff
|
tree
2016-03-03
Ber
k
Hess
Use SIMD transpose scatter in bo
n
deds
commit
|
commitdiff
|
tree
2016-03-03
Be
r
k
Hess
Use rve
c
4 for l
i
sted forc
e
b
u
f
fer
commit
|
commitdiff
|
tree
2016-02-27
Berk H
e
s
s
Remove epsfac fro
m
GPU kernel in
n
er
-
loo
p
s
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Mi
n
or code reorderi
n
g in
G
P
U
k
er
n
els
commit
|
commitdiff
|
tree
2016-02-26
Berk Hess
Fi
x
compil
a
tion
w
ith
Simd4Float,
w
ithout Simd4Do
u
bl
e
commit
|
commitdiff
|
tree
next